Deep Sequencing of the Rat MCAO Cortexes Reveals Crucial circRNAs Involved in Early Stroke Events and Their Regulatory Networks

Wang, Chengtan; Yang, Yuying; Xu, Mengsi; Mao, Fuxiu; Yang, Peng; Shan, Yuan; Gao, Rui; Gan, Shangquan

doi:10.1155/2021/9942537

Cited by 13 publications

(4 citation statements)

References 85 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Advances in genome sequencing technologies and bioinformatics approaches provide powerful alternatives to overcome such clinical diagnostic challenges ( Wang et al., 2021 ). Metagenomic next-generation sequencing (mNGS) is a culture-independent, hypothesis-independent, broad-spectrum sequencing method, which capable of overcoming the limitations of current diagnostic tests.…”

Section: Introductionmentioning

confidence: 99%

Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease

Wang

You²,

Fu³

et al. 2022

Front. Cell. Infect. Microbiol.

Self Cite

View full text Add to dashboard Cite

BackgroundMetagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.ObjectiveWe critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.MethodsA total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.ResultThe majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was −5.44.ConclusionsIn this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.

show abstract

Section: Introductionmentioning

confidence: 99%

Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease

Wang

You²,

Fu³

et al. 2022

Front. Cell. Infect. Microbiol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…The DNA was then fragmented, end-repaired, and a ligated adapter and PCR amplification were used to construct DNA libraries. The Agilent 2100 Bioanalyzer was used for quality control, and eligible libraries were sequenced as described below[ 8 ].…”

Section: Methodsmentioning

confidence: 99%

Previously unexplored etiology for femoral head necrosis: Metagenomics detects no pathogens in necrotic femoral head tissue

Liu¹,

Li²,

Zhang³

et al. 2022

WJCC

View full text Add to dashboard Cite

BACKGROUND Osteonecrosis of the femoral head (ONFH) is a frequent and refractory disease whose pathogenesis has not yet been elucidated. Infection and other factors that reduce the local blood supply can lead to bone necrosis. AIM To aim of this study was to assess the relationship of ONFH with bone infection by use of metagenomic sequencing. METHODS Twelve patients with idiopathic ONFH and 12 comparable controls who were undergoing hip arthroplasty were followed up in parallel. Necrotic femoral head specimens were collected for bacterial and fungal cultures using standard methods. Bone specimens were subjected to preliminary processing, and metagenomics sequencing of microorganisms was performed. A one-way analysis of variance was used to compare bacterial species in the two groups. RESULTS Bacterial and fungal cultures exhibited no evidence of microbial growth in all isolated necrotic femoral head tissues. We thus performed metagenomic sequencing and classified the species as suspected pathogens or suspected background microorganisms based on known bacterial pathogenicity. There was no evidence of viruses, fungi, parasites, M. tuberculosis complex, or mycoplasma/chlamydia. There were also no significant differences in suspected pathogens or suspected background microorganisms ( P > 0.05). CONCLUSION Although we found no pathogens specific for ONFH in necrotic femoral head tissue, our research provides a foundation for future research on the metagenomics of bone pathogens.

show abstract

“…Based on gene sequencing and KEGG analysis, circRyr2_ 23, circGucy1a2_7, circCamta1_9, circSmad4_4, and cir-cDlgap3_1 play important roles in regulating oxidative stress by accessing Hif-1, Nrf, and VEGF signaling pathways [116]. The downregulation of circGucy1a2_7 and circRyr2_36 that occurs after stroke should spontaneously resist oxidative stress by adsorbing miR-7a5p to regulate Keap1/NRF-2 signaling [116][117][118].…”

Section: Circrna Involves In Oxidative Stress After Ischemiamentioning

confidence: 99%

Pathophysiology of Ischemic Stroke: Noncoding RNA Role in Oxidative Stress

Shen

et al. 2022

Oxidative Medicine and Cellular Longevity

View full text Add to dashboard Cite

Stroke is a neurological disease that causes significant disability and death worldwide. Ischemic stroke accounts for 75% of all strokes. The pathophysiological processes underlying ischemic stroke include oxidative stress, the toxicity of excitatory amino acids, ion disorder, enhanced apoptosis, and inflammation. Noncoding RNAs (ncRNAs) may have a vital role in regulating the pathophysiological processes of ischemic stroke, as confirmed by the altered expression of ncRNAs in blood samples from acute ischemic stroke patients, animal models, and oxygen-glucose-deprived (OGD) cell models. Due to specific changes in expression, ncRNAs can potentially be biomarkers for the diagnosis, treatment, and prognosis of ischemic stroke. As an important brain cell component, glial cells mediate the occurrence and progression of oxidative stress after ischemic stroke, and ncRNAs are an irreplaceable part of this mechanism. This review highlights the impact of ncRNAs in the oxidative stress process of ischemic stroke. It focuses on specific ncRNAs that underlie the pathophysiology of ischemic stroke and have potential as diagnostic biomarkers and therapeutic targets.

show abstract

Deep Sequencing of the Rat MCAO Cortexes Reveals Crucial circRNAs Involved in Early Stroke Events and Their Regulatory Networks

Cited by 13 publications

References 85 publications

Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease

Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease

Previously unexplored etiology for femoral head necrosis: Metagenomics detects no pathogens in necrotic femoral head tissue

Pathophysiology of Ischemic Stroke: Noncoding RNA Role in Oxidative Stress

Contact Info

Product

Resources

About